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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/ea-utils">Debian Med / ea-utils</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ea-utils/-/commit/bff3a9d2a1cfb72703880a09ede3d3f9bf1d5343">bff3a9d2</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-08-04T19:35:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update data
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ea-utils/-/commit/cd3e6335112083a6a2fa21935923e1e6d3542212">cd3e6335</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-08-05T01:09:11+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix copyright
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ea-utils/-/commit/86435aa8608f8dd591b205365182a4d61c6c42f0">86435aa8</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-08-05T01:13:05+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop useless B-D on r-cran-hmisc
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ea-utils/-/commit/2fccc1b2a45b754487d9c6abc918c40d927f99b3">2fccc1b2</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-08-05T01:22:46+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Make build cross-buildable
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ea-utils/-/commit/72e243e9015abeb9cbc77accc7501f671ef4e9bf">72e243e9</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-08-05T01:27:51+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Interim changelog entry
</pre>
</li>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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</li>
<li class="file-stats">
<a href="#0d8181cd8c9dbe68093a8faf79725cbbd10e3e73">
<span class="new-file">
+
debian/patches/cross.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#f5231f7af1c674ac6c02a3f66521836ff0cda468">
debian/tests/data/data.fastq.gz
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/ea-utils/-/compare/4d6e32f2cdc86df737f9cbf39a819f5e11a8fb3d...72e243e9015abeb9cbc77accc7501f671ef4e9bf#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">ea-utils (1.1.2+dfsg-7) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> [ Shruti Sridhar ]</span>
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Team Upload.</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> * Add test data</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> * Add get-test-data script</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * Add autopkgtests</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> * Install docs</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> * Update hardening options</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> -- Shruti Sridhar <shruti.sridhar99@gmail.com> Wed, 04 Aug 2021 20:21:48 +0530</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> - Add test data in d/tests/data</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> - Add d/tests/get-test-data script to fetch test data via script,</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> and update the same when needed</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> - d/docs: Install test README and d/tests/run-unit-test script</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> - d/example: Install test data as example</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> - debian/source/include-binaries: Allow compressed test data binary</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> to be included in source</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * d/p/hardening.patch: Update hardening options</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> [ Nilesh Patra ]</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> * d/control: Drop useless B-D on r-cran-hmisc</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> * d/p/cross.patch: Fix compiler variable to get package cross-building</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> Thu, 05 Aug 2021 01:22:52 +0530</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">ea-utils (1.1.2+dfsg-6) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/ea-utils/-/compare/4d6e32f2cdc86df737f9cbf39a819f5e11a8fb3d...72e243e9015abeb9cbc77accc7501f671ef4e9bf#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,7 +9,6 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libgsl-dev,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> libsparsehash-dev,</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> r-cran-hmisc</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Standards-Version: 4.5.1</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/ea-utils</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/ea-utils.git</span>
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<a href="https://salsa.debian.org/med-team/ea-utils/-/compare/4d6e32f2cdc86df737f9cbf39a819f5e11a8fb3d...72e243e9015abeb9cbc77accc7501f671ef4e9bf#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,10 +14,6 @@ Copyright: © 2011 Erik Aronesty <erik@q32.com></td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> 2010 Illumina, Inc</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">License: MIT</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Files: debian/tests/data/*</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">Copyright: NCBI </span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">License: PD</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Files: razf.c</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Copyright: 2008, Jue Ruan <ruanjue@gmail.com>, Heng Li <lh3@sanger.ac.uk></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">License: BSD-2-clause</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -64,6 +60,10 @@ Copyright: © 2014 Tim Booth <tbooth@ceh.ac.uk></td>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext"> © 2015 Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext">License: MIT</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">Files: debian/tests/data/*</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">Copyright: NCBI</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">License: PD</span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext">License: MIT</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext"> Permission is hereby granted, free of charge, to any person obtaining a copy</span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext"> of this software and associated documentation files (the "Software"), to deal</span>
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<li id="0d8181cd8c9dbe68093a8faf79725cbbd10e3e73">
<a href="https://salsa.debian.org/med-team/ea-utils/-/compare/4d6e32f2cdc86df737f9cbf39a819f5e11a8fb3d...72e243e9015abeb9cbc77accc7501f671ef4e9bf#0d8181cd8c9dbe68093a8faf79725cbbd10e3e73"><strong>debian/patches/cross.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Pass right compiler name to CXX variable</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Nilesh Patra <nilesh@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: 2021-08-05</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -1,7 +1,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> # $Id: Makefile 670 2013-12-13 16:47:07Z earonesty $</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CC=g++</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CXX=g++</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> PREFIX?=/usr</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> BINDIR?=$(PREFIX)/bin</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> CFLAGS?=-O3 -I. </span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="p">@@ -64,21 +64,21 @@</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> cp $< $@</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> %: %.c fastq-lib.cpp fastq-lib.h </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) $(CFLAGS) $(CPPFLAGS) fastq-lib.cpp -o $@ $< $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CFLAGS) $(CPPFLAGS) fastq-lib.cpp -o $@ $< $(LDFLAGS)</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> %: %.cpp fastq-lib.cpp fastq-lib.h</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) $(CFLAGS) $(CPPFLAGS) fastq-lib.cpp -o $@ $< $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CFLAGS) $(CPPFLAGS) fastq-lib.cpp -o $@ $< $(LDFLAGS)</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> %: %.c gcModel.c gcModel.h</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) $(CFLAGS) $(CPPFLAGS) gcModel.c -o $@ $< $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CFLAGS) $(CPPFLAGS) gcModel.c -o $@ $< $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> %: %.cpp gcModel.c gcModel.h</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) $(CFLAGS) $(CPPFLAGS) gcModel.c -o $@ $< $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CFLAGS) $(CPPFLAGS) gcModel.c -o $@ $< $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> # why the libbam.a doesn't work? not sure... *.o works</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> sam-stats: sam-stats.cpp fastq-lib.h</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) $(CFLAGS) $(CPPFLAGS) fastq-lib.cpp $< -lbam -lz -lpthread -o $@ $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CFLAGS) $(CPPFLAGS) fastq-lib.cpp $< -lbam -lz -lpthread -o $@ $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> samtools/libbam.a: samtools/*.c samtools/*.h</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> cd samtools && make libbam.a</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="p">@@ -87,14 +87,14 @@</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> ifeq ($(OS),Windows_NT)</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> echo varcall: not supported yet</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> else</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) $(CFLAGS) $(CPPFLAGS) fastq-lib.cpp tidx/tidx-lib.cpp -o $@ $< -lgsl -lgslcblas $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CFLAGS) $(CPPFLAGS) fastq-lib.cpp tidx/tidx-lib.cpp -o $@ $< -lgsl -lgslcblas $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> fastq-stats: fastq-stats.cpp fastq-lib.cpp gcModel.c</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) $(CFLAGS) $(CPPFLAGS) fastq-lib.cpp gcModel.c -o $@ $< $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CFLAGS) $(CPPFLAGS) fastq-lib.cpp gcModel.c -o $@ $< $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> bam-filter: bam-filter.cpp </span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) $(CFLAGS) $(CPPFLAGS) fastq-lib.cpp -o $@ $< -lbamtools $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CFLAGS) $(CPPFLAGS) fastq-lib.cpp -o $@ $< -lbamtools $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> clean:</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> rm -f *.o $(BIN)</span></pre>
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<a href="https://salsa.debian.org/med-team/ea-utils/-/compare/4d6e32f2cdc86df737f9cbf39a819f5e11a8fb3d...72e243e9015abeb9cbc77accc7501f671ef4e9bf#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">makefile.patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">hardening.patch</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">name-space-conflict.patch</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">cross.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/ea-utils/-/compare/4d6e32f2cdc86df737f9cbf39a819f5e11a8fb3d...72e243e9015abeb9cbc77accc7501f671ef4e9bf#f5231f7af1c674ac6c02a3f66521836ff0cda468"><strong>debian/tests/data/data.fastq.gz</strong></a>
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